This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. This is a two phase project with the first being the optimization of label-free protein quantification for detecting differentially expressed proteins in a transgenic mouse model of breast cancer. The second phase is to use the quantification model to discover novel breast cancer effected proteins. Both phases will use the standard LC-MS/MS platform in use with the proteomics core, but will use statistical experimental design and a novel application of linear mixed models for data analysis.